In recent years, studies using molecular techniques have indicated that as many as 700 taxa may be detected in the oral cavity, about 300 or more in subgingival plaque, most of which were uncultivable or at least not recognized. It is likely that some of these uncultivable taxa may be periodontal pathogens. Thus, Specific Aim 1 will test the hypothesis that cultivated or uncultivated bacterial species, not yet recognized as pathogens, are associated with periodontitis. In a cross-sectional study, subgingival biofilm samples, taken from the mesial aspect of up to 28 teeth in each of 80 periodontally healthy and 120 periodontitis subjects. Each sample will be split and individually examined using two microbiological assessments. The first method, direct checkerboard hybridization using whole genomic DNA probes to 40 species, will provide positive and negative controls for known species that discriminate periodontitis from health. Extensive experience indicates that species such as P. gingivalis and T. forsythia will differ significantly from health to disease while most remaining species will not. The second microarray chip assay will detect the presence of 300 taxa;i.e. essentially all of the frequently detected cultivable and as yet uncultivated subgingival taxa. The second major criterion to distinguish periodontal pathogens from non pathogens is based on the notion that suppression of a pathogen should lead to clinical improvement, while failure to reduce that species would lead to disease progression. This criterion will be utilized in Specific Aim 2 which will examine the effects of periodontal therapy on newly recognized potential periodontal pathogens and clinical parameters. The 120 periodontitis subjects from Specific Aim 1 will be treated by SRP and 2 weeks of systemically administered metronidazole and amoxicillin. Clinical monitoring and microbiological sampling will be repeated 3 months post therapy and the subgingival plaque samples examined by the two microbiological methods as described in SA1. Associations will be sought between changes in levels of each test taxon and clinical response to therapy. Since periodontal diseases are infections, it would be difficult to suggest studies that are more important than defining the causative agent(s) of the diseases. This study will examine the association of the uncultivated group of species to periodontal health and disease, thus taking the critical first steps in discriminating the pathogenic from commensal organisms. The identification of such pathogens should, over time, lead to better diagnosis of disease, optimal treatment strategies for the individual patient, new therapeutic approaches and carefully targeted approaches to prevention.